Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RTF1

Cell type

Cell type Class
Digestive tract
Cell type
DLD-1
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
DLD-1
cell line
DLD-1
cell type
Colorectal adenocarcinoma
genotype
SPT6-AID OsTIR1
treatment
Vehcle 2h
chip antibody
RTF1 (Bethyl # A301-329A)

Sequenced DNA Library

library_name
GSM6102813
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq in human DLD1 cells, ~30 million cells were crosslinked with 1% paraformaldehyde in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples. Chromatin was sonicated with the Covaris E220. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G. For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
39500172
Reads aligned (%)
88.0
Duplicates removed (%)
34.9
Number of peaks
758 (qval < 1E-05)

hg19

Number of total reads
39500172
Reads aligned (%)
87.7
Duplicates removed (%)
35.6
Number of peaks
911 (qval < 1E-05)

Base call quality data from DBCLS SRA